Uploads contain some small files and one large file.
Several smaller files instead of one big file would not reduce upload time; the total upload would be the same and overheads would slightly increase. Uploads can also resume if interrupted. Breaking files into smaller parts would also increase server workload, possibly causing unavailability.

You might not have a good connection to the GPUGrid server.
Your connection bandwidth, contention and reliability depend on your geographical location and your ISP. Most ISP's reduce bandwidth at local peak usage times (Bandwidth throttling), and some ISP's limit transfer rates (traffic/packet shaping).

Smaller tasks contain less information and each task would therefore upload in a shorter time. Averaged over a week however, the long tasks would probably require less bandwidth. If you want, you can configure your preferences from here,http://www.gpugrid.net/prefs.php?subset=project

Edit GPUGRID preferences

Run only the selected applications ACEMD standard
ACEMD beta
ACEMD for long runs (8-12 hours on fastest GPU)